R12 is simply the next component in line after C3, in a Plexi module. There's no change in sound, but it would resume the circuit beyond the burnt trace the OP mentioned.
Yes, this has been done before on the rm amps. I remember them used on a rm100 and rt-250 power amp. You should be fine, if you're concerned about them.
I had both modules at one point. The Egnater is a tad warmer and creamier but, that seems to be my experience with all Egnater modules compared to Synergy or Randall. However, from what I remember, they're both very comparable to each other and can dialed in the same. Since the Synergy...
I am planning a few mods. There's a few synergy modules that are not great and could be better. No crazy, over the top mods though.
As for module schematics...good luck!
Perhaps try contacting Fryette directly. He designed the amp. The irony is that you're choosing an older Fryette (VHT) design over a new one, in order to solve your noise issue.